Everything you wanted to know about small RNA but were afraid to ask

Epigenetic modifications as therapeutic targets in atherosclerosis: a focus on DNA methylation and non-coding RNAs

Significant progress in the diagnosis and treatment of cardiovascular disease (CVD) has been made in the past decade, yet it remains a leading cause of morbidity and mortality globally, claiming an estimated 17.9 million deaths per year. Although encompassing any condition that affects the circulatory system, including thrombotic blockage, stenosis, aneurysms, blood clots and arteriosclerosis (general hardening of the arteries), the most prevalent underlying hallmark of CVD is atherosclerosis; the plaque-associated arterial thickening. Further, distinct CVD conditions have overlapping dysregulated molecular and cellular characteristics which underlie their development and progression, suggesting some common aetiology. The identification of heritable genetic mutations associated with the development of atherosclerotic vascular disease (AVD), in particular resulting from Genome Wide Association Studies (GWAS) studies has significantly improved the ability to identify individuals at risk. However, it is increasingly recognised that environmentally-acquired, epigenetic changes are key factors associated with atherosclerosis development. Increasing evidence suggests that these epigenetic changes, most notably DNA methylation and the misexpression of non-coding, microRNAs (miRNAs) are potentially both predictive and causal in AVD development. This, together with their reversible nature, makes them both useful biomarkers for disease and attractive therapeutic targets potentially to reverse AVD progression. We consider here the association of aberrant DNA methylation and dysregulated miRNA expression with the aetiology and progression of atherosclerosis, and the potential development of novel cell-based strategies to target these epigenetic changes therapeutically.

Nucleic Acid Structure Prediction Including Pseudoknots Through Direct Enumeration of States: A User's Guide to the LandscapeFold Algorithm

Here we detail the LandscapeFold secondary structure prediction algorithm and how it is used. The algorithm was previously described and tested in (Kimchi O et al., Biophys J 117(3):520-532, 2019), though it was not named there. The algorithm directly enumerates all possible secondary structures into which up to two RNA or single-stranded DNA sequences can fold. It uses a polymer physics model to estimate the configurational entropy of structures including complex pseudoknots. We detail each of these steps and ways in which the user can adjust the algorithm as desired. The code is available on the GitHub repository https://github.com/ofer-kimchi/LandscapeFold .

The Role of microRNA in the Development, Diagnosis, and Treatment of Cardiovascular Disease: Recent Developments

Since their discovery in 1993, microRNAs (miRNAs) have emerged as important regulators of many crucial cellular processes, and their dysregulation have been shown to contribute to multiple pathologic conditions, including cardiovascular disease (CVD). miRNAs have been found to regulate the expression of various genes involved in cardiac development and function and in the development and progression of CVD. Many miRNAs are master regulators fine-tuning the expression of multiple, often interrelated, genes involved in inflammation, apoptosis, fibrosis, senescence, and other processes crucial for the development of different forms of CVD. This article presents a review of recent developments in our understanding of the role of miRNAs in the development of CVD and surveys their potential applicability as therapeutic targets and biomarkers to facilitate CVD diagnosis, prognosis, and treatment. There are currently multiple potential miRNA-based therapeutic agents in different stages of development, which can be grouped into two classes: miRNA mimics (replicating the sequence and activity of their corresponding miRNAs) and antagomiRs (antisense inhibitors of specific miRNAs). However, in spite of promising preliminary data and our ever-increasing knowledge about the mechanisms of action of specific miRNAs, miRNA-based therapeutics and biomarkers have yet to be approved for clinical applications. SIGNIFICANCE STATEMENT: Over the last few years microRNAs have emerged as crucial, specific regulators of the cardiovascular system and in the development of cardiovascular disease, by posttranscriptional regulation of their target genes. The minireview presents the most recent developments in this area of research, including the progress in diagnostic and therapeutic applications of microRNAs. microRNAs seem very promising candidates for biomarkers and therapeutic agents, although some challenges, such as efficient delivery and unwanted effects, need to be resolved.

The Complexity of the Mammalian Transcriptome

Draft genome assemblies for multiple mammalian species combined with new technologies to map transcripts from diverse RNA samples to these genomes developed in the early 2000s revealed that the mammalian transcriptome was vastly larger and more complex than previously anticipated. Efforts to comprehensively catalog the identity and features of transcripts present in a variety of species, tissues and cell lines revealed that a large fraction of the mammalian genome is transcribed in at least some settings. A large number of these transcripts encode long non-coding RNAs (lncRNAs). Many lncRNAs overlap or are anti-sense to protein coding genes and others overlap small RNAs. However, a large number are independent of any previously known mRNA or small RNA. While the functions of a majority of these lncRNAs are unknown, many appear to play roles in gene regulation. Many lncRNAs have species-specific and cell type specific expression patterns and their evolutionary origins are varied. While technological challenges have hindered getting a full picture of the diversity and transcript structure of all of the transcripts arising from lncRNA loci, new technologies including single molecule nanopore sequencing and single cell RNA sequencing promise to generate a comprehensive picture of the mammalian transcriptome.

miR-221 Exerts Neuroprotective Effects in Ischemic Stroke by Inhibiting the Proinflammatory Response

BACKGROUND

Ischemic stroke is clearly affected by microRNAs (miRNAs) due to dysfunction of their regulatory networks. Our clinical data confirmed decreased miR-221 levels in plasma collected from patients with acute ischemia compared with plasma from healthy controls. Therefore, we further aimed to demonstrate the regulatory mechanisms by which miR-221 exerts its neuroprotective effects in acute ischemic brain injury.

METHODS

Middle cerebral artery occlusion (MCAO) was used to establish focal cerebral ischemia in adult male C57BL/6 mice. A miR-221 mimic or a negative mimic control was injected by intracerebroventricular administration 24 h prior to MCAO. After 48 h, cerebral infarction volume and neurological scores were calculated, and to determine the extent of neuroprotection by miR-221, neurobehavioral tests were performed. Quantitative real-time PCR, ELISA, and flow cytometry were also performed to identify the expression of inflammation-related cytokines and chemokines as well as infiltration/activation of various immune cells in the brain.

RESULTS

The results showed that MCAO mice treated with a miR-221 mimic exhibited significantly decreased cerebral infarction volume and increased amelioration of behavioral deficits. Moreover, the expression of proinflammatory cytokines (TNF-α, MCP-1, VCAM-1, and IL-6) and chemokines (CCL2 and CCL3) was significantly decreased in the miR-221 mimic-treated group. In addition, the flow cytometry data showed that macrophage infiltration and microglial activation were blocked by miR-221 treatment.

CONCLUSION

our results indicate that miR-221 could decrease brain damage in the setting of acute ischemic stroke by inhibiting the proinflammatory response, which furthered our understanding of the molecular basis of miR-221 and provided a new potential therapeutic target for the treatment of ischemic stroke .

Therapeutic angiogenesis with exosomal microRNAs: an effectual approach for the treatment of myocardial ischemia

Therapeutic angiogenesis presents a potential approach for treating ischemic heart diseases especially in patients who are not appropriate candidates for traditional approaches of revascularization. This approach acts through inducing the neovascularization or maturation of pre-existing collateral vessels into functional arteries to bypass the blocked arteries and restore perfusion to ischemic myocardium. Successful stimulation of local angiogenesis can be established by the cross talk between stem cells, endothelial cells, and cardiomyocytes, which is mainly mediated by paracrine communication accompanied by secreted exosomes. Exosomes are extracellular vesicles carrying a complex of signaling molecules, such as microRNAs (miRs) that can modulate the function of recipient cells. Such particles have been indicated to exert cardioprotective role through providing signaling cues for angiogenesis, an effect ascribed mainly to their miRs content. Exosomal miRs-mediated therapeutic angiogenesis has been under drastic preclinical and clinical studies. In the current review, it was aimed to summarize pro-angiogenic exosomal miRs released by various cell types mediating angiogenesis, including stem cells, endothelial cells, and cardiomyocytes, which appear to exert a therapeutic effect on the myocardial ischemia. In brief, secreted exosomal miRs including miR-210, miR-23a-3p, miR-424, let-7f, miR-30b, miR-30c, miR-126, miR-21, miR-132, miR-130a-3p, miR-214, miR-378, miR-126, miR-133, and let-7b-5p could protect against myocardial ischemia through inducing cardiac angiogenesis and vascular regeneration resulting in the increase blood flow to ischemic myocardium.

The Expression of miRNAs in Human Ovaries, Oocytes, Extracellular Vesicles, and Early Embryos: A Systematic Review

The recent discovery of microRNAs (miRNAs) in human reproductive tissues and cells indicates a possible functional role in reproductive function. However, the studies published to date in female reproductive tissues/cells and embryos are inconclusive and sometimes controversial. In order to update the knowledge of this field, the present study aimed to discuss, through a systematic review, the role of miRNAs in female human reproduction and early embryogenesis. We conducted a systematic review of the published literature in MEDLINE and EMBASE databases through June 2018 (plus a complementary search until July 2019), in accordance with the PRISMA guidelines. We have included descriptive and observational studies, in which fertile/infertile women were well-defined. The primary outcome was the miRNA expression in ovaries, oocytes, extracellular vesicles, and embryos. We identified 25,204 articles, of which 28 were selected for qualitative analysis: 18 in ovaries and extracellular vesicles, three in oocytes, and seven in embryos. The present systematic review of descriptive and observational studies demonstrates that aberrant miRNA expression in female reproductive tissues/cells and embryos is related with infertility and embryogenesis errors. The expression of specific miRNAs, particularly in extracellular vesicles, may be used in the future as biomarkers of infertility and prognostic tools of embryo development.

Animal Models of Inflammation for Screening of Anti-inflammatory Drugs: Implications for the Discovery and Development of Phytopharmaceuticals

Inflammation is one of the common events in the majority of acute as well as chronic debilitating diseases and represent a chief cause of morbidity in today's era of modern lifestyle. If unchecked, inflammation leads to development of rheumatoid arthritis, diabetes, cancer, Alzheimer's disease, and atherosclerosis along with pulmonary, autoimmune and cardiovascular diseases. Inflammation involves a complex network of many mediators, a variety of cells, and execution of multiple pathways. Current therapy for inflammatory diseases is limited to the steroidal and non-steroidal anti-inflammatory agents. The chronic use of these drugs is reported to cause severe adverse effects like gastrointestinal, cardiovascular, and renal abnormalities. There is a massive need to explore new anti-inflammatory agents with selective action and lesser toxicity. Plants and isolated phytoconstituents are promising and interesting sources of new anti-inflammatories. However, drug development from natural sources has been linked with hurdles like the complex nature of extracts, difficulties in isolation of pure phytoconstituents, and the yield of isolated compounds in minute quantities that is insufficient for subsequent lead development. Although various in-vivo and in-vitro models for anti-inflammatory drug development are available, judicious selection of appropriate animal models is a vital step in the early phase of drug development. Systematic evaluation of phytoconstituents can facilitate the identification and development of potential anti-inflammatory leads from natural sources. The present review describes various techniques of anti-inflammatory drug screening with its advantages and limitations, elaboration on biological targets of phytoconstituents in inflammation and biomarkers for the prediction of adverse effects of anti-inflammatory drugs. The systematic approach proposed through present article for anti-inflammatory drug screening can rationalize the identification of novel phytoconstituents at the initial stage of drug screening programs.

The matrix environmental and cell mechanical properties regulate cell migration and contribute to the invasive phenotype of cancer cells

The minimal structural unit of a solid tumor is a single cell or a cellular compartment such as the nucleus. A closer look inside the cells reveals that there are functional compartments or even structural domains determining the overall properties of a cell such as the mechanical phenotype. The mechanical interaction of these living cells leads to the complex organization such as compartments, tissues and organs of organisms including mammals. In contrast to passive non-living materials, living cells actively respond to the mechanical perturbations occurring in their microenvironment during diseases such as fibrosis and cancer. The transformation of single cancer cells in highly aggressive and hence malignant cancer cells during malignant cancer progression encompasses the basement membrane crossing, the invasion of connective tissue, the stroma microenvironments and transbarrier migration, which all require the immediate interaction of the aggressive and invasive cancer cells with the surrounding extracellular matrix environment including normal embedded neighboring cells. All these steps of the metastatic pathway seem to involve mechanical interactions between cancer cells and their microenvironment. The pathology of cancer due to a broad heterogeneity of cancer types is still not fully understood. Hence it is necessary to reveal the signaling pathways such as mechanotransduction pathways that seem to be commonly involved in the development and establishment of the metastatic and mechanical phenotype in several carcinoma cells. We still do not know whether there exist distinct metastatic genes regulating the progression of tumors. These metastatic genes may then be activated either during the progression of cancer by themselves on their migration path or in earlier stages of oncogenesis through activated oncogenes or inactivated tumor suppressor genes, both of which promote the metastatic phenotype. In more detail, the adhesion of cancer cells to their surrounding stroma induces the generation of intracellular contraction forces that deform their microenvironments by alignment of fibers. The amplitude of these forces can adapt to the mechanical properties of the microenvironment. Moreover, the adhesion strength of cancer cells seems to determine whether a cancer cell is able to migrate through connective tissue or across barriers such as the basement membrane or endothelial cell linings of blood or lymph vessels in order to metastasize. In turn, exposure of adherent cancer cells to physical forces, such as shear flow in vessels or compression forces around tumors, reinforces cell adhesion, regulates cell contractility and restructures the ordering of the local stroma matrix that leads subsequently to secretion of crosslinking proteins or matrix degrading enzymes. Hence invasive cancer cells alter the mechanical properties of their microenvironment. From a mechanobiological point-of-view, the recognized physical signals are transduced into biochemical signaling events that guide cellular responses such as cancer progression after the malignant transition of cancer cells from an epithelial and non-motile phenotype to a mesenchymal and motile (invasive) phenotype providing cellular motility. This transition can also be described as the physical attempt to relate this cancer cell transitional behavior to a T1 phase transition such as the jamming to unjamming transition. During the invasion of cancer cells, cell adaptation occurs to mechanical alterations of the local stroma, such as enhanced stroma upon fibrosis, and therefore we need to uncover underlying mechano-coupling and mechano-regulating functional processes that reinforce the invasion of cancer cells. Moreover, these mechanisms may also be responsible for the awakening of dormant residual cancer cells within the microenvironment. Physicists were initially tempted to consider the steps of the cancer metastasis cascade as single events caused by a single mechanical alteration of the overall properties of the cancer cell. However, this general and simple view has been challenged by the finding that several mechanical properties of cancer cells and their microenvironment influence each other and continuously contribute to tumor growth and cancer progression. In addition, basement membrane crossing, cell invasion and transbarrier migration during cancer progression is explained in physical terms by applying physical principles on living cells regardless of their complexity and individual differences of cancer types. As a novel approach, the impact of the individual microenvironment surrounding cancer cells is also included. Moreover, new theories and models are still needed to understand why certain cancers are malignant and aggressive, while others stay still benign. However, due to the broad variety of cancer types, there may be various pathways solely suitable for specific cancer types and distinct steps in the process of cancer progression. In this review, physical concepts and hypotheses of cancer initiation and progression including cancer cell basement membrane crossing, invasion and transbarrier migration are presented and discussed from a biophysical point-of-view. In addition, the crosstalk between cancer cells and a chronically altered microenvironment, such as fibrosis, is discussed including the basic physical concepts of fibrosis and the cellular responses to mechanical stress caused by the mechanically altered microenvironment. Here, is highlighted how biophysical approaches, both experimentally and theoretically, have an impact on classical hallmarks of cancer and fibrosis and how they contribute to the understanding of the regulation of cancer and its progression by sensing and responding to the physical environmental properties through mechanotransduction processes. Finally, this review discusses various physical models of cell migration such as blebbing, nuclear piston, protrusive force and unjamming transition migration modes and how they contribute to cancer progression. Moreover, these cellular migration modes are influenced by microenvironmental perturbances such as fibrosis that can induce mechanical alterations in cancer cells, which in turn may impact the environment. Hence, the classical hallmarks of cancer need to be refined by including biomechanical properties of cells, cell clusters and tissues and their microenvironment to understand mechano-regulatory processes within cancer cells and the entire organism.

Upregulation of AKT1 and downregulation of AKT3 caused by dysregulation of microRNAs contributes to pathogenesis of hemangioma by promoting proliferation of endothelial cells

This study aimed to verify the differentially expressed miRNAs (microRNAs) in hemangioma, and explore their roles in the pathogenesis of hemangioma in vivo and ex vivo. Real-time polymerase chain reaction (PCR) and western blot were used to measure reported differentially expressed miRNAs and their potential targets. In-silicon analysis and luciferase assay were conducted to find the target of miR-15a and miR-205. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and flowcytometry were performed to examine the effect of dysregulation of miR-15a and miR-205 on the proliferation and apoptosis of endothelial cells. Among all candidate miRNAs, only miR-205 level was significantly downregulated whereas miR-15a was evidently upregulated in the hemangioma group. Accordingly, AKT3 was validated to be the direct target of miR-15a and miR-205. Using real-time PCR, the level of AKT1 was much higher in hemangioma group, whereas level of AKT3 was much lower in the hemangioma group, and in general expression level of ATK was upregulated in the hemangioma group. Furthermore, the ATK1 level of cells transfected with miR-205 mimics and ATK1 siRNA was substantially downregulated, and anti-miR-205 mimic significantly improved the level of AKT1, and meanwhile the level of ATK3 and PTEN were remarkably suppressed after transfection with miR-15a mimics and ATK3 siRNA, whereas notably overexpressed after introduction of anti-miR-15a. And miR-15a, AKT3 siRNA and anti-miR-205 evidently induced viability, and miR-205, AKT1 siRNA, and anti-miR-15a obviously promoted apoptosis of cells. CONCLUSION: miR-15a and miR-205 had different expression in hemangioma, may be novel therapeutic targets in the treatment of hemangioma by targeting AKT3 and AKT1.

Cardioprotective microRNAs: Lessons from stem cell-derived exosomal microRNAs to treat cardiovascular disease

The stem cell-based therapy has emerged as a promising therapeutic strategy for treating cardiovascular ischemic diseases (CVIDs), such as myocardial infarction (MI). However, some important functional shortcomings of stem cell transplantation, such as immune rejection, tumorigenicity and infusional toxicity, have overshadowed stem cell therapy in the setting of cardiovascular diseases (CVDs). Accumulating evidence suggests that the therapeutic effects of transplanted stem cells are predominately mediated by secreting paracrine factors, importantly, microRNAs (miRs) present in the secreted exosomes. Therefore, novel cell-free therapy based on the stem cell-secreted exosomal miRs can be considered as a safe and effective alternative tool to stem cell therapy for the treatment of CVDs. Stem cell-derived miRs have recently been found to transfer, via exosomes, from a transplanted stem cell into a recipient cardiac cell, where they regulate various cellular process, such as proliferation, apoptosis, stress responses, as well as differentiation and angiogenesis. The present review aimed to summarize cardioprotective exosomal miRs secreted by transplanted stem cells from various sources, including embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), mesenchymal stem cells (MSCs), and cardiac stem/progenitor cells, which showed beneficial modulatory effects on the myocardial infracted heart. In summary, stem cell-exosomal miRs, including miR-19a, mirR-21, miR-21-5p, miR-21-a5p, miR-22 miR-24, miR-26a, miR-29, miR-125b-5p, miR-126, miR-201, miR-210, and miR-294, have been shown to have cardioprotective effects by enhancing cardiomyocyte survival and function and attenuating cardiac fibrosis. Additionally, MCS-exosomal miRs, including miR-126, miR-210, miR-21, miR-23a-3p and miR-130a-3p, are found to exert cardioprotective effects through induction of angiogenesis in ischemic heart after MI.

Exploring the molecular pathogenesis and biomarkers of high risk oral premalignant lesions on the basis of long noncoding RNA expression profiling by serial analysis of gene expression

Oral premalignant lesions (OPLs) have malignant transformation potential, with no reliable markers available. This study aimed to assess molecular events to identify biomarkers that can reflect high-risk lesions as predictive factors to tailor clinical decision for patients on the basis of long noncoding RNAs (lncRNA) expression profiling by serial analysis of gene expression. The GSE31021 and GSE8127 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) and lncRNAs were identified using the LIMMA package in R language. The genes targeted by lncRNAs were predicted among screened DEGs using Pearson's correlation. Gene ontology function and Kyoto Encyclopedia of Genes and Genomes pathway analyses were carried out for genes targeted by lncRNAs using the Database for Annotation, Visualization, and Integrated Discovery online tool. A total of 674 DEGs and differentially expressed lncRNAs were screened. Thirty-two interactions of 10 lncRNAs and 524 target genes were predicted. The lncRNA NEAT1 was among the top 10 lncRNAs. The coregulated target genes RP4-684O24, RP11-283I3, and RP11-350G8 were significantly enriched in the immune response and mannosyl-oligosaccharide mannosidase activity. The target genes coregulated by LINC00665 and MIR378D2 were significantly enriched in the ubiquitin-dependent protein catabolic process, ubiquitin-protein ligase activity, and neurotrophin signaling. The lncRNA NEAT1 may play an important role in high-risk lesions. The novel lncRNAs and DEGs identified in OPLs may mediate the immune response and neurotrophin signaling and show ubiquitin ligase activity. These results improve our understanding of the molecular pathogenesis of OPLs and identify some potential targets for early diagnosis of high risk OPLs.

Neural stem cell therapies and hypoxic-ischemic brain injury

Hypoxic-ischemic brain injury is a significant cause of morbidity and mortality in the adult as well as in the neonate. Extensive pre-clinical studies have shown promising therapeutic effects of neural stem cell-based treatments for hypoxic-ischemic brain injury. There are two major strategies of neural stem cell-based therapies: transplanting exogenous neural stem cells and boosting self-repair of endogenous neural stem cells. Neural stem cell transplantation has been proved to improve functional recovery after brain injury through multiple by-stander mechanisms (e.g., neuroprotection, immunomodulation), rather than simple cell-replacement. Endogenous neural stem cells reside in certain neurogenic niches of the brain and response to brain injury. Many molecules (e.g., neurotrophic factors) can stimulate or enhance proliferation and differentiation of endogenous neural stem cells after injury. In this review, we first present an overview of neural stem cells during normal brain development and the effect of hypoxic-ischemic injury on the activation and function of endogenous neural stem cells in the brain. We then summarize and discuss the current knowledge of strategies and mechanisms for neural stem cell-based therapies on brain hypoxic-ischemic injury, including neonatal hypoxic-ischemic brain injury and adult ischemic stroke.

Inhibition of microRNA-210 suppresses pro-inflammatory response and reduces acute brain injury of ischemic stroke in mice

Stroke is a leading cause of mortality and chronic neurologic disability. Yet, the successful treatment remains limited. In this study, we investigated the efficacy and the mechanism of a novel treatment, microRNA-210 (miR-210) inhibition, in protecting acute ischemic brain injury in adult mice. Focal cerebral ischemia was induced by middle cerebral artery occlusion (MCAO) in adult male C57BL/6 mice. MiR-210-LNA (miR-210 inhibitor) or the negative control was administered via intracerebroventricular injection 24h prior or 4h after MCAO. Cerebral infarction volume and behavioral deficits were determined 48h after MCAO. The expression of inflammation-related genes and infiltration/activation of various immune cells in the brain were assessed by RT-qPCR, flow cytometry, and immunohistochemistry. Acute ischemic stroke significantly increased miR-210 levels in the brain, which was abolished by miR-210-LNA administered prior to MCAO. Pre- and post-MCAO treatments with miR-210-LNA significantly decreased cerebral infarction and ameliorated behavioral deficits induced by MCAO. Long-term behavioral recovery was also improved by miR-210-LNA post-treatment. At the same time, inhibition of miR-210 significantly reduced the expression of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) and chemokines (CCL2 and CCL3), but had no significant effect on anti-inflammatory factors (TGF-β and IL-10). In addition, MCAO-induced macrophage infiltration and microglial activation in the brain were inhibited by the miR-210-LNA treatment. In summary, inhibition of miR-210 suppresses pro-inflammatory response and reduces brain damage in the acute phase of ischemic stroke, providing new insight in molecular basis of a novel therapeutic strategy of miR-210 inhibition in the treatment of acute ischemic stroke.

ICRP Publication 131: Stem Cell Biology with Respect to Carcinogenesis Aspects of Radiological Protection

This report provides a review of stem cells/progenitor cells and their responses to ionising radiation in relation to issues relevant to stochastic effects of radiation that form a major part of the International Commission on Radiological Protection's system of radiological protection. Current information on stem cell characteristics, maintenance and renewal, evolution with age, location in stem cell 'niches', and radiosensitivity to acute and protracted exposures is presented in a series of substantial reviews as annexes concerning haematopoietic tissue, mammary gland, thyroid, digestive tract, lung, skin, and bone. This foundation of knowledge of stem cells is used in the main text of the report to provide a biological insight into issues such as the linear-no-threshold (LNT) model, cancer risk among tissues, dose-rate effects, and changes in the risk of radiation carcinogenesis by age at exposure and attained age. Knowledge of the biology and associated radiation biology of stem cells and progenitor cells is more developed in tissues that renew fairly rapidly, such as haematopoietic tissue, intestinal mucosa, and epidermis, although all the tissues considered here possess stem cell populations. Important features of stem cell maintenance, renewal, and response are the microenvironmental signals operating in the niche residence, for which a well-defined spatial location has been identified in some tissues. The identity of the target cell for carcinogenesis continues to point to the more primitive stem cell population that is mostly quiescent, and hence able to accumulate the protracted sequence of mutations necessary to result in malignancy. In addition, there is some potential for daughter progenitor cells to be target cells in particular cases, such as in haematopoietic tissue and in skin. Several biological processes could contribute to protecting stem cells from mutation accumulation: (a) accurate DNA repair; (b) rapidly induced death of injured stem cells; (c) retention of the DNA parental template strand during divisions in some tissue systems, so that mutations are passed to the daughter differentiating cells and not retained in the parental cell; and (d) stem cell competition, whereby undamaged stem cells outcompete damaged stem cells for residence in the niche. DNA repair mainly occurs within a few days of irradiation, while stem cell competition requires weeks or many months depending on the tissue type. The aforementioned processes may contribute to the differences in carcinogenic radiation risk values between tissues, and may help to explain why a rapidly replicating tissue such as small intestine is less prone to such risk. The processes also provide a mechanistic insight relevant to the LNT model, and the relative and absolute risk models. The radiobiological knowledge also provides a scientific insight into discussions of the dose and dose-rate effectiveness factor currently used in radiological protection guidelines. In addition, the biological information contributes potential reasons for the age-dependent sensitivity to radiation carcinogenesis, including the effects of in-utero exposure.

Transition from inflammation to proliferation: a critical step during wound healing

The ability to rapidly restore the integrity of a broken skin barrier is critical and is the ultimate goal of therapies for hard-to-heal-ulcers. Unfortunately effective treatments to enhance healing and reduce scarring are still lacking. A deeper understanding of the physiology of normal repair and of the pathology of delayed healing is a prerequisite for the development of more effective therapeutic interventions. Transition from the inflammatory to the proliferative phase is a key step during healing and accumulating evidence associates a compromised transition with wound healing disorders. Thus, targeting factors that impact this phase transition may offer a rationale for therapeutic development. This review summarizes mechanisms regulating the inflammation-proliferation transition at cellular and molecular levels. We propose that identification of such mechanisms will reveal promising targets for development of more effective therapies.

Integrative meta-analysis identifies microRNA-regulated networks in infantile hemangioma

BACKGROUND

Hemangioma is a common benign tumor in the childhood; however our knowledge about the molecular mechanisms of hemangioma development and progression are still limited. Currently, microRNAs (miRNAs) have been shown as gene expression regulators with an important role in disease pathogenesis. Our goals were to identify miRNA-mRNA expression networks associated with infantile hemangioma.

METHODS

We performed a meta-analysis of previously published gene expression datasets including 98 hemangioma samples. Deregulated genes were further used to identify microRNAs as potential regulators of gene expression in infantile hemangioma. Data were integrated using bioinformatics methods, and genes were mapped in proteins, which were then used to construct protein-protein interaction networks.

RESULTS

Deregulated genes play roles in cell growth and differentiation, cell signaling, angiogenesis and vasculogenesis. Regulatory networks identified included microRNAs miR-9, miR-939 and let-7 family; these microRNAs showed the most number of interactions with deregulated genes in infantile hemangioma, suggesting that they may have an important role in the molecular mechanisms of disease. Additionally, results were used to identify drug-gene interactions and druggable gene categories using Drug-Gene Interaction Database. We show that microRNAs and microRNA-target genes may be useful biomarkers for the development of novel therapeutic strategies for patients with infantile hemangioma.

CONCLUSIONS

microRNA-regulated pathways may play a role in infantile hemangioma development and progression and may be potentially useful for future development of novel therapeutic strategies for patients with infantile hemangioma.

Extracellular vesicle microRNA transfer in cardiovascular disease

microRNAs (miRNAs) are a class of small regulatory RNAs that decrease protein translation to fine-tune cellular function. Recently, miRNAs were found to transfer from a donor cell into a recipient cell via exosomes and microparticles. These microvesicles are found in blood, urine, saliva, and other fluid compartments. miRNAs are delivered with intact functionality and have been repeatedly shown to regulate protein expression in recipient cells in a paracrine fashion. Thus, transported miRNAs are a new class of cell-to-cell regulatory species. Exosomal miRNA transfer is now being reported in cardiovascular systems and disease. In the blood vessels, this transfer modulates atherosclerosis and angiogenesis. In the heart, it modulates heart failure, myocardial infarction, and response to ischemic preconditioning. This review describes our current understanding of extracellular vesicle miRNA transfer, demonstrating the roles of miR-126, miR-146a, miR-143, and other miRNAs being shuttled from endothelial cells, stem cells, fibroblasts and others into myocytes, endothelial cells, and smooth muscle cells to activate cellular changes and modulate disease phenotypes.

Increased chronic lymphocytic leukemia proliferation upon IgM stimulation is sustained by the upregulation of miR-132 and miR-212

To assess the involvement of microRNAs (miRNAs) in B-cell receptor (BCR) stimulation, we first evaluated miRNA profiling following IgM cross-linking in chronic lymphocytic leukemia (CLL) cells and in normal B lymphocytes. Second, we combined miRNA and gene expression data to identify putative miRNA functional networks. miRNA profiling showed distinctive patterns of regulation after stimulation in leukemic versus normal B lymphocytes and identified a differential responsiveness to BCR engagement in CLL subgroups according to the immunoglobulin heavy chain variable region mutational status and clinical outcome. The most significantly modulated miRNAs in stimulated CLL are miR-132 and miR-212. Notably, these miRNAs appeared regulated in progressive but not in stable CLL. Accordingly, gene profiling showed a significant transcriptional response to stimulation exclusively in progressive CLL. Based on these findings, we combined miRNA and gene expression data to investigate miR-132 and miR-212 candidate interactions in this CLL subgroup. Correlation analysis pointed to a link between these miRNAs and RB/E2F and TP53 cascades with proproliferative effects, as corroborated by functional analyses. Finally, basal levels of miR-132 and miR-212 were measured in an independent cohort of 20 unstimulated CLL cases and both showed lower expression in progressive compared to stable patients, suggesting an association between the expression of these molecules and disease prognosis. Overall, our results support a model involving miR-132 and miR-212 upregulation in sustaining disease progression in CLL. These miRNAs may therefore provide new valuable strategies for therapeutic intervention.

MicroRNAs Related to Polycystic Ovary Syndrome (PCOS)

Polycystic ovary syndrome (PCOS) is the most common, though heterogeneous, endocrine aberration in women of reproductive age, with high prevalence and socioeconomic costs. The syndrome is characterized by polycystic ovaries, chronic anovulation and hyperandrogenism, as well as being associated with infertility, insulin resistance, chronic low-grade inflammation and an increased life time risk of type 2 diabetes. MicroRNAs (miRNAs) are small, non-coding RNAs that are able to regulate gene expression at the post-transcriptional level. Altered miRNA levels have been associated with diabetes, insulin resistance, inflammation and various cancers. Studies have shown that circulating miRNAs are present in whole blood, serum, plasma and the follicular fluid of PCOS patients and that they might serve as potential biomarkers and a new approach for the diagnosis of PCOS. In this review, recent work on miRNAs with respect to PCOS will be summarized. Our understanding of miRNAs, particularly in relation to PCOS, is currently at a very early stage, and additional studies will yield important insight into the molecular mechanisms behind this complex and heterogenic syndrome.

New insights into the expression profile and function of micro-ribonucleic acid in human spermatozoa

OBJECTIVE

To characterize the microRNA (miRNA) expression profile in spermatozoa from human fertile individuals and their implications in human fertility.

DESIGN

The expression levels of 736 miRNAs were evaluated using TaqMan arrays. Ontologic analyses were performed to determine the presence of enriched biological processes among their targets.

SETTING

University research and clinical institutes.

PATIENT(S)

Ten individuals with normal seminogram, standard karyotype, and proven fertility.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Expression levels of 736 miRNAs, presence of enriched metabolic routes among their targets, homogeneity of the population, influence of demographic features in the results, presence of miRNA stable pairs, and best miRNA normalizing candidates.

RESULT(S)

A total of 221 miRNAs were consistently present in all individuals, 452 were only detected in some individuals, and 63 did not appear in any sample. The ontologic analysis of the 2,356 potential targets of the ubiquitous miRNAs showed an enrichment of processes related to cell differentiation, development, morphogenesis, and embryogenesis. None of the miRNAs were significantly correlated with age, semen volume, sperm concentration, motility, or morphology. Correlations between samples were statistically significant, indicating a high homogeneity of the population. A set of 48 miRNA pairs displayed a stable expression, a particular behavior that is discussed in relationship to their usefulness as fertility biomarkers. Hsa-miR-532-5p, hsa-miR-374b-5p, and hsa-miR-564 seemed to be the best normalizing miRNA candidates.

CONCLUSION(S)

Human sperm contain a stable population of miRNAs potentially related to embryogenesis and spermatogenesis.

Nonclinical Safety Biomarkers of Drug-induced Vascular Injury

Better biomarkers are needed to identify, characterize, and/or monitor drug-induced vascular injury (DIVI) in nonclinical species and patients. The Predictive Safety Testing Consortium (PSTC), a precompetitive collaboration of pharmaceutical companies and the U.S. Food and Drug Administration (FDA), formed the Vascular Injury Working Group (VIWG) to develop and qualify translatable biomarkers of DIVI. The VIWG focused its research on acute DIVI because early detection for clinical and nonclinical safety monitoring is desirable. The VIWG developed a strategy based on the premise that biomarkers of DIVI in rat would be translatable to humans due to the morphologic similarity of vascular injury between species regardless of mechanism. The histomorphologic lexicon for DIVI in rat defines degenerative and adaptive findings of the vascular endothelium and smooth muscles, and characterizes inflammatory components. We describe the mechanisms of these changes and their associations with candidate biomarkers for which advanced analytical method validation was completed. Further development is recommended for circulating microRNAs, endothelial microparticles, and imaging techniques. Recommendations for sample collection and processing, analytical methods, and confirmation of target localization using immunohistochemistry and in situ hybridization are described. The methods described are anticipated to aid in the identification and qualification of translational biomarkers for DIVI.

The dark matter rises: the expanding world of regulatory RNAs

The ability to sequence genomes and characterize their products has begun to reveal the central role for regulatory RNAs in biology, especially in complex organisms. It is now evident that the human genome contains not only protein-coding genes, but also tens of thousands of non-protein coding genes that express small and long ncRNAs (non-coding RNAs). Rapid progress in characterizing these ncRNAs has identified a diverse range of subclasses, which vary widely in size, sequence and mechanism-of-action, but share a common functional theme of regulating gene expression. ncRNAs play a crucial role in many cellular pathways, including the differentiation and development of cells and organs and, when mis-regulated, in a number of diseases. Increasing evidence suggests that these RNAs are a major area of evolutionary innovation and play an important role in determining phenotypic diversity in animals.

Vitamin E-gene interactions in aging and inflammatory age-related diseases: implications for treatment. A systematic review

Aging is a complex biological phenomenon in which the deficiency of the nutritional state combined with the presence of chronic inflammation and oxidative stress contribute to the development of many age-related diseases. Under this profile, the free radicals produced by the oxidative stress lead to a damage of DNA, lipids and proteins with subsequent altered cellular homeostasis and integrity. In young-adult age, the cell has a complex efficient system to maintain a proper balance between the levels of free radicals and antioxidants ensuring the integrity of cellular components. In contrast, in old age this balance is poorly efficient compromising cellular homeostasis. Supplementation with Vitamin E can restore the balance and protect against the deteriorating effects of oxidative stress, progression of degenerative diseases, and aging. Experiments in cell cultures and in animals have clearly shown that Vitamin E has a pivotal role as antioxidant agent against the lipid peroxidation on cell membranes preserving the tissue cells from the oxidative damage. Such a role has been well documented in immune, endothelial, and brain cells from old animals describing how the Vitamin E works both at cytoplasmatic and nuclear levels with an influence on many genes related to the inflammatory/immune response. All these findings have supported a lot of clinical trials in old humans and in inflammatory age-related diseases with however contradictory and inconsistent results and even indicating a dangerous role of Vitamin E able to affect mortality. Various factors can contribute to all the discrepancies. Among them, the doses and the various isoforms of Vitamin E family (α,β,γ,δ tocopherols and the corresponding tocotrienols) used in different trials. However, the more plausible gap is the poor consideration of the Vitamin E-gene interactions that may open new roadmaps for a correct and personalized Vitamin E supplementation in aging and age-related diseases with satisfactory results in order to reach healthy aging and longevity. In this review, this peculiar nutrigenomic and/or nutrigenetic aspect is reported and discussed at the light of specific polymorphisms affecting the Vitamin E bioactivity.

Reaction of small heat-shock proteins to different kinds of cellular stress in cultured rat hippocampal neurons

Upregulation of small heat-shock proteins (sHsps) in response to cellular stress is one mechanism to increase cell viability.We previously described that cultured rat hippocampal neurons express five of the 11 family members but only upregulate two of them (HspB1 and HspB5) at the protein level after heat stress. Since neurons have to cope with many other pathological conditions, we investigated in this study the expression of all five expressed sHsps on mRNA and protein level after sublethal sodium arsenite and oxidative and hyperosmotic stress. Under all three conditions, HspB1, HspB5, HspB6, and HspB8 but not HspB11 were consistently upregulated but showed differences in the time course of upregulation. The increase of sHsps always occurred earlier on mRNA level compared with protein levels. We conclude from our data that these four upregulated sHsps (HspB1, HspB5, HspB6, HspB8) act together in different proportions in the protection of neurons from various stress conditions.

A systematic experimental evaluation of microRNA markers of human bladder cancer

BACKGROUND

MicroRNAs (miRNAs) are a class of small RNAs that regulate gene expression. They are aberrantly expressed in many human cancers and are potential therapeutic targets and molecular biomarkers.

METHODS

In this study, we for the first time validated the reported data on the entire set of published differential miRNAs (102 in total) through a series of transcriptome-wide experiments. We have conducted genome-wide miRNA profiling in 17 urothelial carcinoma bladder tissues and in nine normal urothelial mucosa samples using three methods: (1) An Illumina HT-12 microarray hybridization (MA) analysis (2) a suppression-subtractive hybridization (SSH) assay followed by deep sequencing (DS) and (3) DS alone.

RESULTS

We show that DS data correlate with previously published information in 87% of cases, whereas MA and SSH data have far smaller correlations with the published information (6 and 9% of cases, respectively). qRT-PCR tests confirmed reliability of the DS data.

CONCLUSIONS

Based on our data, MA and SSH data appear to be inadequate for studying differential miRNA expression in the bladder.

IMPACT

We report the first comprehensive validated database of miRNA markers of human bladder cancer.

MicroRNAs in Cerebral Ischemia

The risk of ischemic stroke increases substantially with age, making it the third leading cause of death and the leading cause of long-term disability in the world. Numerous studies demonstrated that genes, RNAs, and proteins are involved in the occurrence and development of stroke. Current studies found that microRNAs (miRNAs or miRs) are also closely related to the pathological process of stroke. miRNAs are a group of short, noncoding RNA molecules playing important role in posttranscriptional regulation of gene expression and they have emerged as regulators of ischemic preconditioning and ischemic postconditioning. Here we give an overview of the expression and function of miRNAs in the brain, miRNAs as biomarkers during cerebral ischemia, and clinical applications and limitations of miRNAs. Future prospects of miRNAs are also discussed.

MicroRNA as a diagnostic tool in fine-needle aspiration biopsy of thyroid nodules

Thyroid cancer accounts for 1.5% of all malignancies in the U.S., and it is the most common endocrine malignancy. Detection of thyroid cancer mostly relies on evaluation of thyroid nodules, which are very common but only 5%-7% harbor malignancy. Fine-needle aspiration biopsy (FNAB) is currently the most important tool for the evaluation of thyroid nodules; however, it is limited in that it provides only a cytology assessment of the aspirated cells, and indeterminate diagnoses are present in up to 30% of FNAB results. This limitation can be overcome by the molecular analysis of FNAB, and more specifically with the use of microRNAs (miRs). miRs constitute a class of endogenous small noncoding RNA fragments that regulate gene expression, and in vitro studies have shown that miRs play a significant role in cancer and regulate major processes, such as proliferation, differentiation, and cell death. Several studies have investigated the miR expression signature in different thyroid cancers, and data support its use as a diagnostic tool that is highly accurate for thyroid nodules. The purpose of this study is to review the accumulated data on miR dysregulation in the different thyroid cancer types, critically assess its diagnostic utility, and conclude with future study strategies.

LNA-based oligonucleotide electrotransfer for miRNA inhibition

Micro-RNAs (miRNAs) are small regulatory RNAs that play an important role in disease development and progression and therefore represent a potential new class of therapeutic targets. However, an effective and safe clinical approach for miRNA inhibition remains elusive, primarily due to the lack of effective delivery methods. We proposed to inhibit miRNA by electrotransferring an antisense DNA oligomer containing locked nucleic acids (LNAs) (LNA/DNA oligomer). We observed that electropulsation (EP) led to a strong cellular uptake of LNA/DNA oligomer. The LNA/DNA oligomer electrotransfer mechanism and intracellular localization were visually investigated in real time at the single-cell level. Cyanine 5-labeled oligonucleotide entered exclusively during pulse application on the side of the permeabilized cell membrane facing the cathode, driven by electrophoretic forces. Minutes after the electrotransfer, the LNA/DNA oligomer diffused into the nucleus. EP provided the anti-miRNA oligomer with immediate and direct access to its cytoplasmic mature miRNA target and/or its nuclear precursor miRNA target. We then demonstrated using a LNA/DNA oligomer anti-miR34a that LNA/DNA oligomer electrotransfer decreased the level of the miR34a target and induced its functional inhibition. Our findings show that using the electrotransfer technique for LNA-based oligonucleotide delivery is a promising therapeutic strategy to silence deleterious miRNAs overexpressed in diseases.

MicroRNA expression profiling in archival tissue specimens: methods and data processing

The discovery that the human genome codes for thousands (if not millions) of previously unrecognized non-protein coding RNAs with regulatory functions has changed our understanding of many physiological and pathological processes. A prominent class of non-coding RNAs with important functions in cancer initiation and progression comprised by very short single-stranded, mRNA translation modulating RNAs, termed microRNAs. The determination of microRNA expression profiles is now widely used in biology and pathology, employing a range of methodologies. A steadily growing number of studies describe the analysis of formalin-fixed paraffin-embedded, so-called "archival" specimens. However, procedures for data processing and calculations are far from standardized and differ considerably between published studies, making comparisons and meta-analyses still quite difficult. In this review, we provide a short overview of profiling methods used for archival samples and describe in detail a modified method for normalization and processing of raw data obtained by fluorescence-labeled bead technology from Luminex.Inc.

Differentiating benign from malignant thyroid nodules using micro ribonucleic acid amplification in residual cells obtained by fine needle aspiration biopsy

BACKGROUND

Fine needle aspiration biopsy (FNAB) is the most commonly used diagnostic tool to differentiate benign from malignant thyroid nodules. Nevertheless, some FNAB cytology results are not definite. In such cases diagnostic thyroid lobectomy is performed with malignancy rate on final histopathology ranging at 15%-75%. The aim of this study was to improve on the accuracy of FNAB-based cytology by amplification of microRNAs (micro ribonucleic acids [miRs]) from the residual cells left in the FNAB needle after submission for cytology.

METHODS

Residual cells were collected from the needle cup after FNAB cytology of 77 consecutive patients with thyroid nodules. miR-enriched RNA was extracted for all patients with cytology showing either follicular lesion or suspicion for malignancy (n=11). The expression of miR-21, -31, -146b, -187, -221, and -222 was determined using real-time polymerase chain reaction. Results were compared with final surgical histopathology.

RESULTS

RNA was successfully extracted from all FNAB specimens. Five patients had FNAB cytology suspicious for malignancy. The miR panel was positive in all five (100%). Six patients had follicular lesions on FNAB. The miR panel was positive in three of four patients (75%) with confirmed malignancy and was negative in two of two (0%) patients with benign pathology results. This corresponded to a specificity of 100%, sensitivity of 88%, and accuracy of 90%.

CONCLUSIONS

RNA extraction from FNAB residual cells is feasible, and a miR panel amplified from the extracted RNA seems like a promising diagnostic tool in this limited number of patients.

New routes for transgenesis of the mouse

Transgenesis refers to the molecular genetic techniques for directing specific insertions, deletions and point mutations in the genome of germ cells in order to create genetically modified organisms (GMO). Genetic modification is becoming more practicable, efficient and predictable with the development and use of a variety of cell and molecular biology tools and DNA sequencing technologies. A collection of plasmidial and viral vectors, cell-type specific promoters, positive and negative selectable markers, reporter genes, drug-inducible Cre-loxP and Flp/FRT recombinase systems are available which ensure efficient transgenesis in the mouse. The technologies for the insertion and removal of genes by homologous-directed recombination in embryonic stem cells (ES) and generation of targeted gain- and loss-of function alleles have allowed the creation of thousands of mouse models of a variety of diseases. The engineered zinc finger nucleases (ZFNs) and small hairpin RNA-expressing constructs are novel tools with useful properties for gene knockout free of ES manipulation. In this review we briefly outline the different approaches and technologies for transgenesis as well as their advantages and disadvantages. We also present an overview on how the novel integrative mouse and human genomic databases and bioinformatics approaches have been used to understand genotype-phenotype relationships of hundreds of mutated and candidate disease genes in mouse models. The updating and continued improvements of the genomic technologies will eventually help us to unraveling the biological and pathological processes in such a way that they can be translated more efficiently from mouse to human and vise-versa.

Mapping the regulatory sequences controlling 93 breast cancer-associated miRNA genes leads to the identification of two functional promoters of the Hsa-mir-200b cluster, methylation of which is associated with metastasis or hormone receptor status in advanced breast cancer

MicroRNAs (miRNAs) are small non-coding RNAs of ∼20 nt in length that are capable of modulating gene expression post-transcriptionally. Although miRNAs have been implicated in cancer, including breast cancer, the regulation of miRNA transcription and the role of defects in this process in cancer is not well understood. In this study we have mapped the promoters of 93 breast cancer-associated miRNAs, and then looked for associations between DNA methylation of 15 of these promoters and miRNA expression in breast cancer cells. The miRNA promoters with clearest association between DNA methylation and expression included a previously described and a novel promoter of the Hsa-mir-200b cluster. The novel promoter of the Hsa-mir-200b cluster, denoted P2, is located ∼2 kb upstream of the 5′ stemloop and maps within a CpG island. P2 has comparable promoter activity to the previously reported promoter (P1), and is able to drive the expression of miR-200b in its endogenous genomic context. DNA methylation of both P1 and P2 was inversely associated with miR-200b expression in eight out of nine breast cancer cell lines, and in vitro methylation of both promoters repressed their activity in reporter assays. In clinical samples, P1 and P2 were differentially methylated with methylation inversely associated with miR-200b expression. P1 was hypermethylated in metastatic lymph nodes compared with matched primary breast tumours whereas P2 hypermethylation was associated with loss of either oestrogen receptor or progesterone receptor. Hypomethylation of P2 was associated with gain of HER2 and androgen receptor expression. These data suggest an association between miR-200b regulation and breast cancer subtype and a potential use of DNA methylation of miRNA promoters as a component of a suite of breast cancer biomarkers.

MicroRNAs in Human Diseases: From Lung, Liver and Kidney Diseases to Infectious Disease, Sickle Cell Disease and Endometrium Disease

MicroRNAs (miRNAs) are a class of naturally occurring small non-coding RNAs of about 22 nucleotides that have recently emerged as important regulators of gene expression at the posttranscriptional level. Recent studies provided clear evidence that microRNAs are abundant in the lung, liver and kidney and modulate a diverse spectrum of their functions. Moreover, a large number of studies have reported links between alterations of miRNA homeostasis and pathological conditions such as infectious diseases, sickle cell disease and endometrium diseases as well as lung, liver and kidney diseases. As a consequence of extensive participation of miRNAs in normal functions, alteration and/or abnormalities in miRNAs should have importance in human diseases. Beside their important roles in patterning and development, miRNAs also orchestrated responses to pathogen infections. Particularly, emerging evidence indicates that viruses use their own miRNAs to manipulate both cellular and viral gene expression. Furthermore, viral infection can exert a profound impact on the host cellular miRNA expression profile, and several RNA viruses have been reported to interact directly with cellular miRNAs and/or to use these miRNAs to augment their replication potential. Here I briefly summarize the newly discovered roles of miRNAs in various human diseases including infectious diseases, sickle cell disease and enodmetrium diseases as well as lung, liver and kidney diseases.

[Other actors in the oocyte and follicular growth: the role of microRNAs in the cumulus-oocyte dialog]

The good folliculogenesis evolution is fundamental for the obtaining of a competent oocyte, able to lead to pregnancy, once fertilized. During the follicular development, the oocyte is in close contact with surrounding cumulus cells (CCs) to form a cumulus-oocyte complex. The bidirectional exchange between oocyte and contiguous CCs via gap junction communications and paracrine signaling is important for oocyte competence and CCs development. These reciprocal regulations are controlled by some key genes. Recently, it has been demonstrated that these genes are themselves regulated by short RNAs fragments (approximately 22 nucleotides), called microRNAs. The identification and the quantification in the CCs of the microRNAs regulating these genes could promote the development of non invasive tests in order to assess the oocyte quality and its ability to provide embryo with a high implantation potential. This approach could be decisive in the embryo selection to transfer and could avoid the risk of multiple pregnancies by the replacement of a single embryo.

MicroRNAs in Human Diseases: From Autoimmune Diseases to Skin, Psychiatric and Neurodegenerative Diseases

MicroRNAs (miRNAs) are small noncoding RNA molecules that negatively regulate gene expression via degradation or translational repression of their target messenger RNAs (mRNAs). Recent studies have clearly demonstrated that miRNAs play critical roles in several biologic processes, including cell cycle, differentiation, cell development, cell growth, and apoptosis and that miRNAs are highly expressed in regulatory T (Treg) cells and a wide range of miRNAs are involved in the regulation of immunity and in the prevention of autoimmunity. It has been increasingly reported that miRNAs are associated with various human diseases like autoimmune disease, skin disease, neurological disease and psychiatric disease. Recently, the identification of mi- RNAs in skin has added a new dimension in the regulatory network and attracted significant interest in this novel layer of gene regulation. Although miRNA research in the field of dermatology is still relatively new, miRNAs have been the subject of much dermatological interest in skin morphogenesis and in regulating angiogenesis. In addition, miRNAs are moving rapidly onto center stage as key regulators of neuronal development and function in addition to important contributions to neurodegenerative disorder. Moreover, there is now compelling evidence that dysregulation of miRNA networks is implicated in the development and onset of human neruodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, Tourette's syndrome, Down syndrome, depression and schizophrenia. In this review, I briefly summarize the current studies about the roles of miRNAs in various autoimmune diseases, skin diseases, psychoneurological disorders and mental stress.

Identification of miRNAs as potential modulators of tissue factor expression in patients with systemic lupus erythematosus and antiphospholipid syndrome

BACKGROUND

Tissue factor (TF) is the main initiator of the coagulation cascade and elements that may upregulate its expression might provoke thrombotic events. Systemic lupus erythematosus (SLE) and antiphospholipid syndrome (APS) are autoimmune diseases characterized by a high TF expression in monocytes.

OBJECTIVES

To examine the role of microRNAs (miRNAs) in TF expression and to evaluate their levels in SLE and APS patients.

METHODS

An in silico search was performed to find potential putative binding sites of miRNAs in TF mRNA. In vitro validation was performed transfecting cells expressing TF (THP-1 and MDA-MB-231) with oligonucleotide miRNA precursors and inhibitors. Additionally, reporter assays were performed to test for the binding of miR-20a to TF mRNA. Levels of miRNAs and TF were measured by quantitative (qRT-PCR) in patients with APS and SLE.

RESULTS

Overexpression of miRNA precursors, but not inhibitors, of two of the members of cluster miR-17∼92, for example miR-19b and miR-20a, in cells expressing TF decreased TF mRNA, protein levels, and procoagulant activity between 30% and 60%. Reporter assays showed that miR-20a binds to TF mRNA. Finally, we measured levels of miR-19b and miR-20a in monocytes from patients with APS and SLE and observed significantly lower miRNAs levels in comparison with healthy subjects inversely correlated with the levels of TF.

CONCLUSIONS

Down-regulation of miR-19b and miR-20a observed in patients with SLE and APS could contribute to increased TF expression and thus provoke the hypercoagulable state characteristic of these patients.

The Story of SPATA2 (Spermatogenesis-Associated Protein 2): From Sertoli Cells to Pancreatic Beta-Cells

In an attempt to isolate new spermatogenesis-associated genes, pd1 was initially identified and cloned as a novel human cDNA sequence from testis cDNA library. The novel gene was submitted to GenBank under accession n° U28164 in 1996. PD1 expression was demonstrated at the Sertoli cell level with a production which appeared to be under the influence of neighbouring spermatogenic cells. The rat orthologue of human pd1 was further cloned and, according to the Gene Nomenclature Committee, was renamed spata2 (spermatogenesis-associated protein 2) gene on the basis of its FSH-dependent up-regulation and developmental expression. The analysis of the human and rat cDNA sequences disclosed an open reading frame for a protein of 520 and 511 amino acids respectively, with an overall identity of 85%. Subsequently, a zebrafish orthologue of the human spata2 gene was identified. The consensus open reading frame (1650 bp) encodes a polypeptide of 550 amino acids, which shares 37% identity with the human spata2. By means of whole-mount in situ hybridisation it has been shown that spata2 transcripts are maternally derived and become strongly localised in the central nervous system at early developmental stages. At the same time, RT-PCR analysis demonstrated that several adult zebrafish tissues expressed high level of spata2 mRNA providing evidence that this gene may have a broader function than previously described. More recently, novel findings have highlighted a potential role of spata2 during pancreatic development and β-cell proliferation. In this review we will discuss spata2 gene expression and regulation as well as focus on novel evidence, which suggests a role for this protein in pancreatic β-cell function.

MicroRNAs in Human Diseases: From Cancer to Cardiovascular Disease

The great discovery of microRNAs (miRNAs) has revolutionized current cell biology and medical science. miRNAs are small conserved non-coding RNA molecules that post-transcriptionally regulate gene expression by targeting the 3' untranslated region of specific messenger RNAs for degradation or translational repression. New members of the miRNA family are being discovered on a daily basis and emerging evidence has demonstrated that miRNAs play a major role in a wide range of developmental process including cell proliferation, cell cycle, cell differentiation, metabolism, apoptosis, developmental timing, neuronal cell fate, neuronal gene expression, brain morphogenesis, muscle differentiation and stem cell division. Moreover, a large number of studies have reported links between alterations of miRNA homeostasis and pathological conditions such as cancer, psychiatric and neurological diseases, cardiovascular disease, and autoimmune disease. Interestingly, in addition, miRNA deficiencies or excesses have been correlated with a number of clinically important diseases ranging from cancer to myocardial infarction. miRNAs can repress the gene translation of hundreds of their targets and are therefore well-positioned to target a multitude of cellular mechanisms. As a consequence of extensive participation in normal functions, it is quite logical to ask the question if abnormalities in miRNAs should have importance in human diseases. Great discoveries and rapid progress in the past few years on miRNAs provide the hope that miRNAs will in the near future have a great potential in the diagnosis and treatment of many diseases. Currently, an explosive literature has focussed on the role of miRNA in human cancer and cardiovascular disease. In this review, I briefly summarize the explosive current studies about involvement of miRNA in various human cancers and cardiovascular disease.

The Role of MicroRNAs in Regulatory T Cells and in the Immune Response

The discovery of microRNA (miRNA) is one of the major scientific breakthroughs in recent years and has revolutionized current cell biology and medical science. miRNAs are small (19~25nt) noncoding RNA molecules that post-transcriptionally regulate gene expression by targeting the 3' untranslated region (3'UTR) of specific messenger RNAs (mRNAs) for degradation of translation repression. Genetic ablation of the miRNA machinery, as well as loss or degradation of certain individual miRNAs, severely compromises immune development and response, and can lead to immune disorders. Several sophisticated regulatory mechanisms are used to maintain immune homeostasis. Regulatory T (Treg) cells are essential for maintaining peripheral tolerance, preventing autoimmune diseases and limiting chronic inflammatory diseases. Recent publications have provided compelling evidence that miRNAs are highly expressed in Treg cells, that the expression of Foxp3 is controlled by miRNAs and that a range of miRNAs are involved in the regulation of immunity. A large number of studies have reported links between alterations of miRNA homeostasis and pathological conditions such as cancer, cardiovascular disease and diabetes, as well as psychiatric and neurological diseases. Although it is still unclear how miRNA controls Treg cell development and function, recent studies certainly indicate that this topic will be the subject of further research. The specific circulating miRNA species may also be useful for the diagnosis, classification, prognosis of diseases and prediction of the therapeutic response. An explosive literature has focussed on the role of miRNA. In this review, I briefly summarize the current studies about the role of miRNAs in Treg cells and in the regulation of the innate and adaptive immune response. I also review the explosive current studies about clinical application of miRNA.

MicroRNA profiling using fluorescence-labeled beads: data acquisition and processing

The discovery of small regulatory RNA molecules during the last years has changed our understanding of many biological and pathological processes. The most prominent and best analyzed class of these small regulatory noncoding RNAs is composed of the microRNAs. The analysis of microRNA expression patterns is now widely used in biology and pathology employing a range of methodologies. However, procedures for data processing and calculations are far from standardized and differ considerably between published studies. This makes comparisons and meta-analyses still quite difficult. In this chapter, we describe a modified method for normalization and processing of raw data obtained if utilizing fluorescence-labeled bead technology from Luminex. Inc.

MicroRNA profiling using RNA from microdissected immunostained tissue

mRNA expression profiling has been used to define molecular subtypes of human breast cancer. Also microRNAs have been investigated in these breast cancer subtypes. However, little is known regarding the microRNA signature of healthy luminal and basal breast epithelial cells. Therefore, a method is described to isolate immunostained luminal and basal breast epithelial cells in formalin-fixed paraffin-embedded tissues by laser microdissection. Employing this new methodological approach, we could identify distinct microRNA profiles of luminal and basal breast epithelial cells by real-time PCR-based profiling.

Counter-regulation of cholinesterases: differential activation of PKC and ERK signaling in retinal cells through BChE knockdown

The ubiquitous cholinesterase (ChE) enzymes, functioning in the termination of acetylcholine mediated neural transmission, are also reported to have additional functions. Through application of siRNAs against butyrylcholinesterase (BChE) in R28 cells, a retinal cell line with pluripotent properties, a counter-regulation between ChEs was revealed. BChE knock down resulted in an up-regulation of not only acetylcholinesterase (AChE), but also altered the signaling status of PKC and ERK. Knockdown of BChE modified ERK signaling most notably through ERK1/2 proteins, together with the transcription activator P90RSK1 and c-fos. Stimulation of the R28 cell line by forskolin revealed that ChEs are involved in an intricate cross talk between different signaling pathways. Forskolin-stimulated R28 cells displayed a robust cholinergic response, as detected by both electrophysiology and ChE expression, and changed the activation status of PKC/ERK signaling pathways. The findings in R28 cells show that ChE expressions are inversely co-regulated and act through the transcription factors c-fos and P90RSK1. Since R28 cells have the capacity to differentiate into different cell types through stimulation of signaling pathways, ChEs are likely to be associated with cell fate determination, rather than just terminating cholinergic responses.